A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

The question of virginity testing in Turkey

Pre-marital sex for a woman is regarded as wrong in my country. As a result, it is socially forbidden for a woman to engage in this act. In order to present a woman as a virgin on her marriage day, she is subjected to pressure, and put under control both by her family and societal norms. However, a man is free and never made to suffer any of the above. A woman found to be a virgin on her first night of marriage is seen as a normal person while one suspected to have lost her virginity is made to undergo a series of medical examinations to bring clarity to her situation.     

The unfolding of the P pili quaternary structure by stretching is reversible, not plastic

P pili are protein filaments expressed by uropathogenic Escherichia coli that mediate binding to glycolipids on epithelial cell surfaces, which is a prerequisite for bacterial infection. When a bacterium, attached to a cell surface, is exposed to external forces, the pili, which are composed of approximately 10(3) PapA protein subunits arranged in a helical conformation, can elongate by unfolding to a linear conformation. This property is considered important for the ability of a bacterium to withstand shear forces caused by urine flow. It has hitherto been assumed that this elongation is plastic, thus constituting a permanent conformational deformation. We demonstrate, using optical tweezers, that this is not the case; the unfolding of the helical structure to a linear conformation is fully reversible. It is surmised that this reversibility helps the bacteria regain close contact to the host cells after exposure to significant shear forces, which is believed to facilitate their colonization.     

The modelling of fibre reorientation in soft tissue

In this paper, a hyperelastic and thermodynamically consistent model for soft tissue is developed that is able to describe the change of the initial orientation of the collagen fibres. Full numerical implementation is considered as well. The collagen architecture is assumed to reorient driven by a specific thermodynamical force. The anisotropy is described by a strain energy function, which is decomposed into a part related to the matrix and a part related to the fibres. The initial fibre orientation is defined by a structural tensor, while the current orientation is described by a time-dependent structural tensor, which results from the initial one by a rotational transformation. The rotation tensor is obtained via an integration process of a rate tensor, which depends on an adequately defined thermodynamical force. The integration is achieved via an exponential map algorithm, where it is shown that the rotation is necessarily a two-parametric one. Efficiency of the proposed formulation is demonstrated using some numerical examples.     

Image segmentation using a neural network

An object extraction problem based on the Gibbs Random Field model is discussed. The Maximum a'posteriori probability (MAP) estimate of a scene based on a noise-corrupted realization is found to be computationally exponential in nature. A neural network, which is a modified version of that of Hopfield, is suggested for solving the problem. A single neuron is assigned to every pixel. Each neuron is supposed to be connected only to all of its nearest neighbours. The energy function of the network is designed in such a way that its minimum value corresponds to the MAP estimate of the scene. The dynamics of the network are described. A possible hardware realization of a neuron is also suggested. The technique is implemented on a set of noisy images and found to be highly robust and immune to noise.     

Logical Probability and Risk Assessment

A risk assessment is intended to provide a statement of current knowledge which is intended to inform a decision-maker of the current state of knowledge in response to a particular concern. Because answering the concerns of decision-makers often requires inferences to be drawn, doubt often arises over how the inference is to be drawn. In quantitative risk assessment, where a mathematical equation or model is used to draw the inference, this uncertainty is referred to as model uncertainty. A two-step process, which is referred to as logical probability, is proposed as a technique for representing model uncertainty in a risk assessment. The first step involves assigning model weights in which the degree of evidential support for each of the alternative models is considered. The second step involves assigning a unique interval in the range of 0 to 1 for each model which reflects the models' weight, to form a probability distribution. While the second step is straightforward, the first step is not. Assigning model weights requires consideration of any line of evidence that may reasonably impact the validity of the assertion of a model. While the development of a procedure for doing so may be expected to be a process which reflects the subjective preferences of whomever is involved in creating it, there are some historical precedents on which to build. Foremost among these are (1) the use of a correlation coefficient or other goodness-of-fit criteria to measure the degree of correspondence between a given model and a set of observations which are used as evidence to support it, and (2) preference given to models which are simpler, which may be ascertained as the number of adjustable parameters the model contains. Additional principles, which have little or no tradition to stand on, must be used to reflect the impact of other empirically supported beliefs on model preference. The procedure proposed is comparable to the procedure known as decision analysis, in which probabilities are assigned to alternative models based on expert or subjective input. The principal difference in the present case is that it is suggested that principles which transcend the decision at hand should be sought and articulated in order to generate a consistent measure of uncertainty arising from interpretation.     

A conserved region within the Bordetella pertussis autotransporter BrkA is necessary for folding of its passenger domain

Autotransporter secretion represents a unique mechanism that Gram-negative bacteria employ to deliver proteins to their cell surface. BrkA is a Bordetella pertussis autotransporter protein that mediates serum resistance and contributes to adherence of the bacterium to host cells. BrkA is a 103 kDa protein that is cleaved to form a 73 kDa alpha-domain and a 30 kDa beta domain. The alpha domain, also referred to as the passenger domain, is responsible for the effector functions of the protein, whereas the beta domain serves as a transporter. In an effort to characterize BrkA secretion, we have shown that BrkA has a 42 amino acid signal peptide for transit across the cytoplasmic membrane, and a translocation unit made up of a short linker region fused to the beta-domain to ferry the passenger domain to the bacterial surface through a channel formed by the beta-domain. In this report, we provide genetic, biochemical and structural evidence demonstrating that a region within the BrkA passenger (Glu601-Ala692) is necessary for folding the passenger. This region is not required for surface display in the outer membrane protease OmpT-deficient Escherichia coli strain UT5600. However, a BrkA mutant protein bearing a deletion in this region is susceptible to digestion when expressed in E. coli strains expressing OmpT suggesting that the region is required to maintain a stable structure. The instability of the deletion mutant can be rescued by surface expressing Glu601-Ala692in trans suggesting that this region is acting as an intramolecular chaperone to effect folding of the passenger concurrent with or following translocation across the outer membrane.     

A Slow Rotary Shaker for Embedding in Viscous Media

Embedding vessels are carried by a metal tray which has a tilt of about 20° to the horizontal plane. The tray is supported by a shaft attached perpendicular to its bottom. The shaft passes loosely through a hole in a rigid plate and is attached by a ball joint to a crank, which is driven at about 20 rev/min by a geared-down electric motor. Thus a combined tilting and rotary motion is imparted to the tray to produce a continuous flow of the embedding medium about the specimens.     

A centrosomal theory of the short term evolutionary maintenance of sexual reproduction

A new mode of inheritance is postulated in which a sexual offspring receives a contribution from each parent and selects the better to pass on to its own offspring. This could provide a simple advantage to sex over a sex whose magnitude is shown to be of the order of a doubling of fitness in each generation, large enough to cancel the twofold cost of sex. This possible advantage to sex can be realized only if a cell component is in fact inherited in this selectively ambiguous way. No such component is known of, but the eukaryotic centrosome is a possible candidate. The possibility is discussed that the centrosome contains an obligatorily non-digital replicator which has an essential function in the initiation of microtubules. If this theory is true, it has the capacity to apply as widely as sex is found, and it would rescue theories of the long-term maintenance of sex from the necessity to provide a twofold advantage in each generation. If false, the theory will soon be disproved.     

Evolutionary equilibrium strategies.

This paper re-examines the concept of evolutionary stability proposed by Maynard Smith.For any finite population it is shown that a strategy which is stable in the sense of Maynard Smith may have a lower fitness than a mutant strategy regardless of the proportion of contestants using the latter.Two alternative concepts of evolutionary stability are then proposed. A strategy is described as being strongly stable if no mutant is able to invade because of its higher fitness and weakly stable if it has a higher fitness whenever the contestants using any particular mutant strategy become sufficiently numerous.For the “war of attrition” between contestants of a given species Maynard Smith and others have argued that the evolutionarily stable strategy is for a contestant to bid (for food or territory) by attempting to wait out its opponent according to an exponential mixed strategy. This paper establishes that such a strategy is only weakly stable and that for any number n there exists a mutant strategy with a higher fitness until the number of mutants in the population exceeds n.The final section reconsiders the stability issue when a natural informational asymmetry is introduced. Each contestant is assumed to be uncertain as to the value its opponent places on the object over which they are competing. In contrast to the symmetric case it is shown that there is a strategy which is strongly stable with respect to any feasible mutant as long as the population is sufficiently large.     

The Influence of Temperature on the Effect of Bacteriostatic Concentrations of Phenol Against Escherichia coli

S ummary . During early exponential growth of Escherichia coli in the absence of phenol there is a natural death rate at 20, 30, and 44° but at the optimum temperature around 37° there is little if any significant death. The influence of a rise in temperature from 20 to 44° is to decrease the generation time and at 44° the lower generation time compensates for a reduced generation index. The main effect of sub-bacteriostatic concentrations of phenol is to increase the generation time but at 30, 37 and 44° there is a significant reduction in the generation index at the higher concentrations resulting in a dynamic bacteriostasis. At 20° bacteriostasis is due mainly to a large generation time but there is a little growth and so bacteriostasis is essentially dynamic. There is also evidence to suggest that the effect of a particular concentration of phenol on the generation index is not merely influenced by the temperature but by the generation time under the particular set of conditions. If phenol is added to rapidly growing cultures of E. coli the effect of a rise in temperature is to reduce the concentration required for bacteriostasis but if it is added during the lag phase there is a maximum in the bacteriostatic concentration between 20 and 37°.     

Forming sparse representations by local anti-Hebbian learning

How does the brain form a useful representation of its environment? It is shown here that a layer of simple Hebbian units connected by modifiable anti-Hebbian feed-back connections can learn to code a set of patterns in such a way that statistical dependency between the elements of the representation is reduced, while information is preserved. The resulting code is sparse, which is favourable if it is to be used as input to a subsequent supervised associative layer. The operation of the network is demonstrated on two simple problems.     

The PCM–basal body/primary cilium coalition

The centrosome is an organelle that acts as a microtubule-organizing center (MTOC) throughout the cell cycle. Within the centrosome are often two components that each have an ability to organize microtubule structures: the centriole that has the potential to function as a basal body and nucleate a cilium or a flagellum and a mass of protein material that in the presence of a centriole is commonly referred to as the pericentriolar material (PCM) that organizes cytoplasmic and spindle microtubule arrays. One characteristic of a large variety of cells is the ability to express a non-motile primary cilium. It is now appreciated that the function of the primary cilium is integral to a variety of essential cell functions and defects affecting this structure underlie a variety of human disease. While the function of the primary cilium and manner in which a basal body organizes a primary cilium has received extensive attention there is now a need to explore the inter-relationship between the PCM and the basal body/primary cilium. It is this latter topic that is the focus of this review where we show that the PCM is integrated with the centriole to form a coalition that is essential for both the expression and function of the primary cilium as well as the organization and function of the cellular environment that surrounds it.     

Design of a Virtual Player for Joint Improvisation with Humans in the Mirror Game

Joint improvisation is often observed among humans performing joint action tasks. Exploring the underlying cognitive and neural mechanisms behind the emergence of joint improvisation is an open research challenge. This paper investigates jointly improvised movements between two participants in the mirror game, a paradigmatic joint task example. First, experiments involving movement coordination of different dyads of human players are performed in order to build a human benchmark. No designation of leader and follower is given beforehand. We find that joint improvisation is characterized by the lack of a leader and high levels of movement synchronization. Then, a theoretical model is proposed to capture some features of their interaction, and a set of experiments is carried out to test and validate the model ability to reproduce the experimental observations. Furthermore, the model is used to drive a computer avatar able to successfully improvise joint motion with a human participant in real time. Finally, a convergence analysis of the proposed model is carried out to confirm its ability to reproduce joint movements between the participants.     

Glycosylphosphatidylinositol-anchored fungal polysaccharide in Aspergillus fumigatus

Galactomannan is a characteristic polysaccharide of the human filamentous fungal pathogen Aspergillus fumigatus that can be used to diagnose invasive aspergillosis. In this study, we report the isolation of a galactomannan fraction associated to membrane preparations from A. fumigatus mycelium by a lipid anchor. Specific chemical and enzymatic degradations and mass spectrometry analysis showed that the lipid anchor is a glycosylphosphatidylinositol (GPI). The lipid part is an inositol phosphoceramide containing mainly C18-phytosphingosine and monohydroxylated lignoceric acid (2OH-C(24:0) fatty acid). GPI glycan is a tetramannose structure linked to a glucosamine residue: Manalpha1-2Manalpha1-2Manalpha1-6Manalpha1-4GlcN. The galactomannan polymer is linked to the GPI structure through the mannan chain. The GPI structure is a type 1, closely related to the one previously described for the GPI-anchored proteins of A. fumigatus. This is the first time that a fungal polysaccharide is shown to be GPI-anchored.     

Simple sequential boundaries for treatment selection in multi-armed randomized clinical trials with a control

Summary .   In situations when many regimens are possible candidates for a large phase III study, but too few resources are available to evaluate each relative to the standard, conducting a multi-armed randomized selection trial is a useful strategy to remove inferior treatments from further consideration. When the study has a relatively quick endpoint such as an imaging-based lesion volume change in acute stroke patients, frequent interim monitoring of the trial is ethically and practically appealing to clinicians. In this article, I propose a class of sequential selection boundaries for multi-armed clinical trials, in which the objective is to select a treatment with a clinically significant improvement upon the control group, or to declare futility if no such treatment exists. The proposed boundaries are easy to implement in a blinded fashion, and can be applied on a flexible monitoring schedule in terms of calendar time. Design calibration with respect to prespecified levels of confidence is simple, and can be accomplished when the response rate of the control group is known only up to an interval. One of the proposed methods is applied to redesign a selection trial with an imaging endpoint in acute stroke patients, and is compared to an optimal two-stage design via simulations: The proposed method imposes smaller sample size on average than the two-stage design; this advantage is substantial when there is in fact a superior treatment to the control group.     

Proton-dependent electron transfer from CuA to heme a and altered EPR spectra in mutants close to heme a of cytochrome oxidase

Eukaryotic cytochrome c oxidase (CcO) and homologous prokaryotic forms of Rhodobacter and Paraccocus differ in the EPR spectrum of heme a. It was noted that a histidine ligand of heme a (H102) is hydrogen bonded to serine in Rhodobacter (S44) and Paraccocus CcOs, in contrast to glycine in the bovine enzyme. Mutation of S44 to glycine shifts the heme a EPR signal from g(z) = 2.82 to 2.86, closer to bovine heme a at 3.03, without modifying other properties. Mutation to aspartate, however, results in an oppositely shifted and split heme a EPR signal of g(z) = 2.72/2.78, accompanied by lower activity and drastically inhibited intrinsic electron transfer from CuA to heme a. This intrinsic rate is biphasic; the proportion that is slow is pH dependent, as is the relative intensity of the two EPR signal components. At pH 8, the heme a EPR signal at 2.72 is most intense, and the electron transfer rate (CuA to heme a) is 10-130 s(-1), compared to wild-type at 90,000 s(-1). At pH 5.5, the signal at 2.78 is intensified, and a biphasic rate is observed, 50% fast (approximately wild type) and 50% slow (90 s(-1)). The data support the prediction that the hydrogen-bonding partner of the histidine ligand of heme a is one determinant of the EPR spectral difference between bovine and bacterial CcO. We further demonstrate that the heme a redox potential can be dramatically altered by a nearby carboxyl, whose protonation leads to a proton-coupled electron transfer process.     

Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis

Serial ligation is the repeated reversible binding of a ligand to one receptor after another. It is a widespread phenomenon throughout biochemical systems, occurring anytime receptors are clustered together and ligand binding is reversible. Computer simulations are used in this work to investigate a representative example, which is the serial ligation of an extracellular aspartate molecule to the membrane-bound chemotaxis receptors of an Escherichia coli bacterium. It is found that the initial binding site of a ligand to a cluster of receptors is more likely to be near the edge of the cluster than near the middle, although there is no overall bias when all rebindings are considered. Serial ligation does not lead directly to signal amplification or attenuation but instead causes binding events to be correlated in both space and time: a ligand is likely to bind many times in rapid succession in a small region of the receptor cluster, but there can also be long intervals between bindings. This leads to an increased level of noise in the received signal but may allow a single ligand to be sensed above a uniform level of background noise. The focus of this paper is on the interpretation of simulation results so they can be generalized to a wide variety of other systems and to allow the identification of systems in which serial ligation is likely to be important. In the process, several characteristic times are identified, as are scaling laws for the spatial and temporal dynamics.     

Fluorescence polarization immunoassay: detection of antibody to Brucella abortus

Fluorescence polarization immunoassay (FPA) is a homogeneous immunoassay useful for rapid and accurate detection of antibody or antigen. The principle of the assay is that a fluorescent dye (attached to an antigen or an antibody fragment) can be excited by plane-polarized light at the appropriate wavelength. As a rule, a small molecule rotates faster when in solution than a larger molecule. The rotation rate may be assessed by measuring light intensity in the vertical and horizontal planes. Generally, the time it takes a molecule to rotate through a given angle is an indication of its size. When a small molecule that rotates rapidly is bound to a larger molecule, the rotation rate is decreased and this decrease is measured. Because it is a primary antigen-antibody interaction, the rate of reaction is very rapid and usually a result may be obtained in minutes. This technology was applied to the detection of antibody to Brucella abortus in serum and milk, providing for the first time a rapid primary binding assay that is cost effective for use in the field.     

A role for apolipoprotein(a) in protection of the low-density lipoprotein component of lipoprotein(a) from copper-mediated oxidation

Low-density lipoprotein (LDL) oxidation is stimulated by copper. Addition of a recombinant form of apolipoprotein(a) (apo(a); the distinguishing protein component of lipoprotein(a)) containing 17 plasminogen kringle IV-like domains (17K r-apo(a)) protects LDL against oxidation by copper. Protection is specific to apo(a) and is not achieved by plasminogen or serum albumin. When Cu(2+) is added to 17K r-apo(a), its intrinsic fluorescence is quenched in a concentration-dependent and saturable manner. Quenching is unchanged whether performed aerobically or anaerobically and is reversible by ethylenediaminetetraacetate, suggesting that it is due to equilibrium binding of Cu(2+) and not to oxidative destruction of tryptophan residues. The fluorescence change exhibits a sigmoid dependence on copper concentration, and time courses of quenching are complex. At copper concentrations below 10 microM there is little quenching, whereas above 10 microM quenching proceeds immediately as a double-exponential decay. The affinity and kinetics of copper binding to 17K r-apo(a) are diminished in the presence of the lysine analogue epsilon -aminocaproic acid. We propose that copper binding to the kringle domains of 17K is mediated by a His-X-His sequence that is located about 5A from the closest tryptophan residue of the lysine binding pocket. Copper binding may account for the natural resistance to copper-mediated oxidation of lipoprotein(a) relative to LDL that has been previously reported and for the protection afforded by apo(a) from copper-mediated oxidation of LDL that we describe in the present study.